fdnamove Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. Function Interactive DNA parsimony Description Interactive construction of phylogenies from nucleic acid sequences, with their evaluation by parsimony and compatibility and the display of reconstructed ancestral bases. This can be used to find parsimony or compatibility estimates by hand. Algorithm DNAMOVE is an interactive DNA parsimony program, inspired by Wayne Maddison and David and Wayne Maddison's marvellous program MacClade, which is written for Macintosh computers. DNAMOVE reads in a data set which is prepared in almost the same format as one for the DNA parsimony program DNAPARS. It allows the user to choose an initial tree, and displays this tree on the screen. The user can look at different sites and the way the nucleotide states are distributed on that tree, given the most parsimonious reconstruction of state changes for that particular tree. The user then can specify how the tree is to be rearraranged, rerooted or written out to a file. By looking at different rearrangements of the tree the user can manually search for the most parsimonious tree, and can get a feel for how different sites are affected by changes in the tree topology. This program uses graphic characters that show the tree to best advantage on some computer systems. Its graphic characters will work best on MSDOS systems or MSDOS windows in Windows, and to any system whose screen or terminals emulate ANSI standard terminals such as old Digital VT100 terminals, Telnet programs, or VT100-compatible windows in the X windowing system. For any other screen types, (such as Macintosh windows) there is a generic option which does not make use of screen graphics characters. The program will work well in those cases, but the tree it displays will look a bit uglier. This program carries out unrooted parsimony (analogous to Wagner trees) (Eck and Dayhoff, 1966; Kluge and Farris, 1969) on DNA sequences. The method of Fitch (1971) is used to count the number of changes of base needed on a given tree. The assumptions of this method are exactly analogous to those of MIX: 1. Each site evolves independently. 2. Different lineages evolve independently. 3. The probability of a base substitution at a given site is small over the lengths of time involved in a branch of the phylogeny. 4. The expected amounts of change in different branches of the phylogeny do not vary by so much that two changes in a high-rate branch are more probable than one change in a low-rate branch. 5. The expected amounts of change do not vary enough among sites that two changes in one site are more probable than one change in another. That these are the assumptions of parsimony methods has been documented in a series of papers of mine: (1973a, 1978b, 1979, 1981b, 1983b, 1988b). For an opposing view arguing that the parsimony methods make no substantive assumptions such as these, see the papers by Farris (1983) and Sober (1983a, 1983b), but also read the exchange between Felsenstein and Sober (1986). Change from an occupied site to a deletion is counted as one change. Reversion from a deletion to an occupied site is allowed and is also counted as one change. Usage Here is a sample session with fdnamove % fdnamove Interactive DNA parsimony Input (aligned) nucleotide sequence set(s): dnamove.dat Phylip tree file (optional): NEXT (R # + - S . T U W O F H J K L C ? X Q) (? for Help): Q Do you want to write out the tree to a file? (Y or N): Y 5 species, 13 sites Computing steps needed for compatibility in sites ... (unrooted) 19.0 Steps 11 sites compatible ,-----------5:Epsilon --9 ! ,--------4:Delta `--8 ! ,-----3:Gamma `--7 ! ,--2:Beta `--6 `--1:Alpha Tree written to file "dnamove.treefile" Go to the input files for this example Go to the output files for this example Command line arguments Interactive DNA parsimony Version: EMBOSS:6.6.0.0 Standard (Mandatory) qualifiers: [-sequence] seqsetall (Aligned) nucleotide sequence set(s) filename and optional format, or reference (input USA) [-intreefile] tree Phylip tree file (optional) Additional (Optional) qualifiers (* if not always prompted): -weights properties Weights file - ignore sites with weight zero -outgrno integer [0] Species number to use as outgroup (Integer 0 or more) -dothreshold toggle [N] Use threshold parsimony * -threshold float [1] Threshold value (Number 1.000 or more) -initialtree menu [Arbitary] Initial tree (Values: a (Arbitary); u (User); s (Specify)) -screenwidth integer [80] Width of terminal screen in characters (Any integer value) -screenlines integer [24] Number of lines on screen (Any integer value) -outtreefile outfile [*.fdnamove] Phylip tree output file (optional) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-sequence" associated qualifiers -sbegin1 integer Start of each sequence to be used -send1 integer End of each sequence to be used -sreverse1 boolean Reverse (if DNA) -sask1 boolean Ask for begin/end/reverse -snucleotide1 boolean Sequence is nucleotide -sprotein1 boolean Sequence is protein -slower1 boolean Make lower case -supper1 boolean Make upper case -scircular1 boolean Sequence is circular -squick1 boolean Read id and sequence only -sformat1 string Input sequence format -iquery1 string Input query fields or ID list -ioffset1 integer Input start position offset -sdbname1 string Database name -sid1 string Entryname -ufo1 string UFO features -fformat1 string Features format -fopenfile1 string Features file name "-outtreefile" associated qualifiers -odirectory string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messages -version boolean Report version number and exit Input file format fdnamove reads any normal sequence USAs. Input files for usage example File: dnamove.dat 5 13 Alpha AACGUGGCCA AAU Beta AAGGUCGCCA AAC Gamma CAUUUCGUCA CAA Delta GGUAUUUCGG CCU Epsilon GGGAUCUCGG CCC Output file format fdnamove outputs a graph to the specified graphics device. outputs a report format file. The default format is ... Output files for usage example File: dnamove.treefile (Epsilon,(Delta,(Gamma,(Beta,Alpha)))); Data files None Notes None. References None. Warnings None. Diagnostic Error Messages None. Exit status It always exits with status 0. Known bugs None. See also Program name Description distmat Create a distance matrix from a multiple sequence alignment ednacomp DNA compatibility algorithm ednadist Nucleic acid sequence distance matrix program ednainvar Nucleic acid sequence invariants method ednaml Phylogenies from nucleic acid maximum likelihood ednamlk Phylogenies from nucleic acid maximum likelihood with clock ednapars DNA parsimony algorithm ednapenny Penny algorithm for DNA eprotdist Protein distance algorithm eprotpars Protein parsimony algorithm erestml Restriction site maximum likelihood method eseqboot Bootstrapped sequences algorithm fdiscboot Bootstrapped discrete sites algorithm fdnacomp DNA compatibility algorithm fdnadist Nucleic acid sequence distance matrix program fdnainvar Nucleic acid sequence invariants method fdnaml Estimate nucleotide phylogeny by maximum likelihood fdnamlk Estimates nucleotide phylogeny by maximum likelihood fdnapars DNA parsimony algorithm fdnapenny Penny algorithm for DNA fdolmove Interactive Dollo or polymorphism parsimony ffreqboot Bootstrapped genetic frequencies algorithm fproml Protein phylogeny by maximum likelihood fpromlk Protein phylogeny by maximum likelihood fprotdist Protein distance algorithm fprotpars Protein parsimony algorithm frestboot Bootstrapped restriction sites algorithm frestdist Calculate distance matrix from restriction sites or fragments frestml Restriction site maximum likelihood method fseqboot Bootstrapped sequences algorithm fseqbootall Bootstrapped sequences algorithm Author(s) This program is an EMBOSS conversion of a program written by Joe Felsenstein as part of his PHYLIP package. Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. History Written (2004) - Joe Felsenstein, University of Washington. Converted (August 2004) to an EMBASSY program by the EMBOSS team. Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None